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/* This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
* See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
* Author(s): Vincent Rouvreau
*
* Copyright (C) 2016 Inria
*
* Modification(s):
* - YYYY/MM Author: Description of the modification
*/
#include <boost/program_options.hpp>
#include <CGAL/Epick_d.h>
#include <gudhi/Alpha_complex.h>
#include <gudhi/Persistent_cohomology.h>
// to construct a simplex_tree from alpha complex
#include <gudhi/Simplex_tree.h>
#include <iostream>
#include <string>
#include <limits> // for numeric_limits
using Simplex_tree = Gudhi::Simplex_tree<>;
using Filtration_value = Simplex_tree::Filtration_value;
void program_options(int argc, char *argv[], std::string &off_file_points, std::string &output_file_diag,
Filtration_value &alpha_square_max_value, int &coeff_field_characteristic,
Filtration_value &min_persistence);
int main(int argc, char **argv) {
std::string off_file_points;
std::string output_file_diag;
Filtration_value alpha_square_max_value;
int coeff_field_characteristic;
Filtration_value min_persistence;
program_options(argc, argv, off_file_points, output_file_diag, alpha_square_max_value, coeff_field_characteristic,
min_persistence);
// ----------------------------------------------------------------------------
// Init of an alpha complex from an OFF file
// ----------------------------------------------------------------------------
using Kernel = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>;
Gudhi::alpha_complex::Alpha_complex<Kernel> alpha_complex_from_file(off_file_points);
Simplex_tree simplex;
if (alpha_complex_from_file.create_complex(simplex, alpha_square_max_value)) {
// ----------------------------------------------------------------------------
// Display information about the alpha complex
// ----------------------------------------------------------------------------
std::cout << "Simplicial complex is of dimension " << simplex.dimension() << " - " << simplex.num_simplices()
<< " simplices - " << simplex.num_vertices() << " vertices." << std::endl;
// Sort the simplices in the order of the filtration
simplex.initialize_filtration();
std::cout << "Simplex_tree dim: " << simplex.dimension() << std::endl;
// Compute the persistence diagram of the complex
Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Gudhi::persistent_cohomology::Field_Zp> pcoh(
simplex);
// initializes the coefficient field for homology
pcoh.init_coefficients(coeff_field_characteristic);
pcoh.compute_persistent_cohomology(min_persistence);
// Output the diagram in filediag
if (output_file_diag.empty()) {
pcoh.output_diagram();
} else {
std::cout << "Result in file: " << output_file_diag << std::endl;
std::ofstream out(output_file_diag);
pcoh.output_diagram(out);
out.close();
}
}
return 0;
}
void program_options(int argc, char *argv[], std::string &off_file_points, std::string &output_file_diag,
Filtration_value &alpha_square_max_value, int &coeff_field_characteristic,
Filtration_value &min_persistence) {
namespace po = boost::program_options;
po::options_description hidden("Hidden options");
hidden.add_options()("input-file", po::value<std::string>(&off_file_points),
"Name of file containing a point set. Format is one point per line: X1 ... Xd ");
po::options_description visible("Allowed options", 100);
visible.add_options()("help,h", "produce help message")(
"output-file,o", po::value<std::string>(&output_file_diag)->default_value(std::string()),
"Name of file in which the persistence diagram is written. Default print in std::cout")(
"max-alpha-square-value,r", po::value<Filtration_value>(&alpha_square_max_value)
->default_value(std::numeric_limits<Filtration_value>::infinity()),
"Maximal alpha square value for the Alpha complex construction.")(
"field-charac,p", po::value<int>(&coeff_field_characteristic)->default_value(11),
"Characteristic p of the coefficient field Z/pZ for computing homology.")(
"min-persistence,m", po::value<Filtration_value>(&min_persistence),
"Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length "
"intervals");
po::positional_options_description pos;
pos.add("input-file", 1);
po::options_description all;
all.add(visible).add(hidden);
po::variables_map vm;
po::store(po::command_line_parser(argc, argv).options(all).positional(pos).run(), vm);
po::notify(vm);
if (vm.count("help") || !vm.count("input-file")) {
std::cout << std::endl;
std::cout << "Compute the persistent homology with coefficient field Z/pZ \n";
std::cout << "of an Alpha complex defined on a set of input points.\n \n";
std::cout << "The output diagram contains one bar per line, written with the convention: \n";
std::cout << " p dim b d \n";
std::cout << "where dim is the dimension of the homological feature,\n";
std::cout << "b and d are respectively the birth and death of the feature and \n";
std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl;
std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
std::cout << visible << std::endl;
exit(-1);
}
}
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